Entering edit mode
2.1 years ago
tinakopale • 0
I am working with WES data and I am trying to build a pipeline with the help of GATK best practices. I would like to know the difference between pipeline that is built-in in Illumina sequencer and GATk Best Practices pipeline.
Is the VQSR used in built in software of Illumina? Why should I follow Best practices when everything is built in sequencer, can you please help me to see the difference?
Thank you very much
If the pipeline built-in in Illumina sequencers you are refering to is the DRAGEN pipeline, then there aren't many differences, and the plan is for them to be the same:
DRAGEN-GATK Update: Let's get more specific
The hardware-accelerated DRAGEN pipeline found in Illumina sequencers is subscription-based, but a lot faster, so it may suit the needs of big sequencing centers and service providers.
Thank you, it is not the Dragan pipeline that is built-in.